In Arabidopsis research, microarrays have typically been employed for the measurement of gene expression under different conditions. Microarray analysis is often used to analyze the effects of the expression of wild-type genes (control) versus mutants, the effects of varying environmental conditions, and the effects of hormones. In addition, microarray analysis is used to analyze differences in gene expression between growth stages and tissues. Other array applications include comparative genomic hybridization, chromatin immunoprecipitation, mutation detection, and genotyping. This chapter focuses on gene expression profiling, which is typically performed by the competitive hybridization of two samples, each labeled with a fluorescent dye such as cyanine 3-CTP or cyanine 5-CTP. We describe the steps, from RNA purification to data analysis, that are involved in obtaining data from DNA microarrays.